Well it's not like you actually SEE her take them, but it's inferred pretty powerfully at the end there.Adult Aya compliments the girl on her eyes, and because we know that Aya is now just as spooky as her dad and likes to take body parts and stuff from people, we can assume that she's gunna take the girl's eyes ;m;

This is my own opinion but I see her as a bit kinder then her father. yes, it does seem that the game implies she takes on her fathers work, but Aya asks the girls name to remember them (fulfilling Dio's wish)

and it really didnt help that her mom was pretty damn crazy tooi mean who in their right mind marries a guy and supports him when he does a bunch of gross experiments like this????the whole family is warped!!! ;A;